Trapped in Torchwood
by Mademoiselle Sinistra
Summary: set in an A/U co-authored with Sherlock's Sparrow The 21st Century is when everything changes, but will they change for the better without the aid of the Doctor?
1. Torchwood's Greatest Capture

**Trapped in Torchwood**

**By: Little Joe's Mistress & Sherlock's Sparrow**

**Disclaimer: **We don't own any characters, places, events or things from _Doctor Who _or _Torchwood._

**Prologue**

_~Torchwood 3-Cardiff, Wales-1899~_

Once they realized their newest prisoner couldn't die, the two ladies of Torchwood Three deemed him a threat and locked the American in a cell in their 'dungeon'.

"He could be useful, Alice," said one, "not staying dead is a valuable asset in our line of work."

"No, Emily," said Alice Guppy, "he can't be trusted under _any _circumstances. He's an ally of the Doctor, and that means a threat to Torchwood. We're keeping him under lock and key."

_Torchwood 3-1941~_

Colonel Rupert Collins was reading the Harkness file again. He found it fascinating, as well as Harkness himself. He decided it was time to pay their immortal a visit. It's been awhile since he'd seen him in person.

Harkness was sitting in the center of his cell and blankly staring out. Col. Collins turned to his medic.

"How is he, Tyler?" he asked.

"He's much improved, Colonel," said Doctor Tyler, "the psychosis appears to be diminishing."

"Damn Torchwood thirty years ago," muttered the colonel, "let me know when he's fit for work."*

Col. Collins wanted Jack Harkness to work for Torchwood and not be its prisoner. He wouldn't be allowed to live off base, but he wouldn't be kept in one of those small cells.

_~Torchwood 3-1951~_

Col. Collins had Jack working for Torchwood with great success. He had rules every member of Torchwood had to follow, to ensure that Harkness wouldn't turn on them. He never went on missions alone, he couldn't carry a weapon, his room was kept locked at night, etc. Dr. Hudson was convinced Jack was still insane, but he was certainly more lucid than in the past.

*

Alex Hopkins had had his murder/suicide thwarted. He managed to kill half the staff, before members of Torchwood One had arrived on New Year's Day. Alex was retconned and sectioned. The surviving members of Torchwood Three were too traumatized to take on the role of leader, so Yvonne Hartman sent someone from Torchwood One to fill Alex's role.

His name was Ianto Jones.

********************

**Chapter One: Torchwood's Greatest Capture**

_~Torchwood 1-London, England-2005~_

After defeating the Sycorax in the Earth's atmosphere, Yvonne Hartman sent agents to investigate near where the ship had been seen. Among the debris of the ship, there was a human-like hand on the ground. It would go back to the lab for analyzing.

_~Torchwood 1-2006~_

Torchwood One was regrouping after the defeat of the Cybermen and Daleks. They had also managed to recapture the Doctor. Blake Dillon had promoted himself to Head of Torchwood One. He wasn't as charitable as Yvonne Hartman and had the Doctor in handcuffs and taken to the cell block. They had emptied all his pockets; which took a surprisingly long time to do; during which time, they confiscated his Sonic Screwdriver and TARDIS key. They locked up the TARDIS somewhere on the premises as well.

_~Christmas Eve~_

A woman named Donna Noble was transported aboard the TARDIS. After some questioning, she was released, but Torchwood had a sample of her blood to examine. She was human, but there was something weird in the sample. They brought the Doctor to the lab to look at the sample.

"Huon particles, but that's impossible," said the Doctor, "the only Huon particles in existence are in the TARDIS."

"Well, apparently, you're wrong about that, Doctor," snapped Blake, "are Huon particles dangerous?"

"No, not in this state," said the Doctor, "but they're alien, so they _must _be a threat to you people."

They eventually drained the particles from Miss Noble and defeated the Empress of the Racnoss. The Doctor reluctantly provided assistance.

Early in 2007, Blake started worrying that the few allies the Doctor had would eventually find him at Torchwood London, so he made a phone call to have the Doctor transported to a more secure location.

"Hello, Mr. Jones? Blake Dillon."

_~Torchwood 3-2007~_

The Doctor was secretly transported to Torchwood Three headquarters. Ianto Jones was there to greet them. Ianto had a hard time believing that the all powerful, dangerous to Britain Doctor was this skinny, frail man in front of him.

"Mr. Dillon, Ianto Jones. Welcome to Torchwood Cardiff," said Ianto, "is this him?"

Blake Dillon nodded briefly in the affirmative.

"Mr. Jones, meet the Doctor," he said, "I've been told one of the Doctor's allies is in employ here. Are you prepared?"

"Captain Harkness will not be told of the Doctor's identity. We are certain he has never seen this incarnation of him," replied Ianto.

"Good."


	2. In the Enemy's Hands

**Chapter Two: In the Enemy's Hands**

_~Torchwood 3-2007~_

The Doctor had a cell in the basement of Torchwood Three. He didn't even have a bed. Just a blanket, a stone floor, three stone walls and a Plexiglas wall with air holes at the top. Jack worked here, but that meant he wasn't likely to help him, since he was working for people who only saw him as a threat to the country. The Doctor sat on the hard floor and sighed as he ran his hands through his hair.

"What are you in for?"

"Torchwood hates me," muttered the Doctor.

A laugh; short harsh and bitter.

"Yeah, welcome to the club. Jack Harkness, by the way. Who are you?"

"John Smith."

"How...ordinary," said Jack.

The Doctor shrugged.

"Ordinary is what makes humans so brilliant!"

***

"Who exactly is 'John Smith'?" Jack asked Ianto.

"Who?" asked Ianto.

"The alien brought over from Torchwood One," said Jack.

"Oh, no one you should be concerned about," replied Ianto.

"What is he?" asked Jack, "he looks human."

"He's not human," said Ianto, "I believe Mr. Dillon said he's the last of his kind."

"There seems to be an awful lot of those running around the universe," muttered Jack, thinhking of the Doctor mentioning being the last Time Lord, "they should make a 'Last of their Kind' Club. They could have t-shirts."

***

The staff that had come from Torchwood One with Ianto, seemed the most hostile to the Doctor. The staff that had always been at Torchwood Three were a bit nicer, but usually not by very much. Jack thought he was cute. And mysterious. And sad. Just sitting in that tiny little cell day after day in a place where people hate you just for not being born on the Earth-or for previously associating with one.

***

The Doctor found Torchwood Three more comfortable than Torchwood One. He got regular meals and bathroom trips, for starters. Torchwood Three also appeared to lack the Torture Chamber of Torchwood One. And, he had a friend-sort of. _Wouldn't be so friendly if I told who I __**really **__am._

_***_

"Where's home?"

"Pardon?"

The Doctor was pulled away from memories of a Certain Blonde.

"Where are you from?"

"You've never been there. Far far away from here. So far away. How about you? Not exactly a native to this little island, are you?"

"Far away, too. Been here a long time. Longer than I care to think about. Long, long time. All alone."

"I'm sorry. It's not easy to be alone. I think I'm cursed with loneliness."

"Just a couple of lone wolves, us, then. 'Lone Wolf' or 'Bad Wolf'? No Bad Wolf. Bad Wolf bad wolf bad wolf. Bad Wolf everywhere! Can't get away-can't hide-can't escape Bad Wolf."

***

Jack was seated on the floor in front of the Doctor's cell, muttering about hidden messages and killer pepperpots and game stations and blue boxes that weren't blue boxes and face changing Doctors. The Doctor got as close to Jack as he could, pressed up against the Plexiglas, staring wide-eyed at him. He opened his mouth to speak, but before a single syallable had time to leave his throat, Jack was escorted out of the Doctor's sight. This was his fault. All his fault. _I'm sorry, Jack. I'm so sorry._

_***_

Jack woke up in his room. There was a polite knock on the door. He recognized the knock.

"Yeah?"

"How are you feeling, Jack? Better?" inquired the beautiful Welsh voice.

Jack smiled. Worked like a charm every time.

"Yep," he answered.

The lock clicked.

"You can come out whenever you want. Door's unlocked now."

"Okay. Thanks."

He hoped he hadn't scared their resident alien too much with his little game. He _had _stayed away from the theatrics because he hadn't wanted to alarm him badly. He supposed he'd go down and see.

***

He looked depressed.

"Hey, sorry about that," said Jack, "did I scare you?"

"No, not really. Worried me; concerned me, yes."

"Why are you so nice?" asked Jack, "I'm keeping you a prisoner here."

"You don't think I belong here, just following orders. Just like your boss. Why are you so nice? I'm an alien threat, you know."

"You're not a threat," said Jack, "just an alien."


End file.
